AgileQualityFilter
Quality control, detagging and reformatting of clonal sequencing data
AgileQualityFilter performs a number of pre-alignment tasks on sequence data
from an Illumina GA-II clonal sequencer. The primary function of AgileQualityFilter
is to remove low quality sequence data before alignment to a reference sequence. It can also performs the secondary roles
of formatting the data from *.qseq.txt, *.fasta or *.fastq files to either the *.fasta or *.fastq file formats. If the
reads are tagged with 5′ index tags (“barcodes”), the program can export the detagged data to a specific file.
AgileQualityFilter reads the PHRED quality string for each sequence and
identifies the position of bases where the quality falls below a user-defined cut-off value. These positions
then become uncalled positions and are subsequently exported as 'N's. It is possible to limit the number of uncalled
positions in a read, with the sequence truncated if it exceeds the user-defined value. It is also possible
to identify reads whose median quality score falls below a user-defined value; these reads can be either rejected or
truncated so that the median quality score of the remaining sequence is no longer below the cut-off value.
Guide
The AgileQualityFilter user guide can be found
here.
Download
The AgileQualityFilter program can be downloaded from my departments web site
here.